Code
if(base::interactive()) {
params <- rmarkdown::yaml_front_matter(here::here("analysis/03_beta_diversity.qmd"))$params
}
factor_of_interest <- params$factor_of_interestWhere we analyse the effect of a factor on local diversity
Date: November 25, 2024
See the documentation of the MiscMetabar package for example of alpha diversity analysis.
if(base::interactive()) {
params <- rmarkdown::yaml_front_matter(here::here("analysis/03_beta_diversity.qmd"))$params
}
factor_of_interest <- params$factor_of_interestlibrary(knitr)
library(targets)
library(MiscMetabar)
here::i_am("analysis/02_alpha_diversity.qmd")
source(here::here("R/styles.R"))d_pq <- clean_pq(tar_read("d_vs", store=here::here("_targets/")))Cleaning suppress 3 taxa and 13 samples.
hill_pq(subset_samples(d_pq, Type %in% c("Mix", "Mono")), factor_of_interest, one_plot = TRUE) &
(
theme_idest(
subtitle_size = 8,
plot_title_size = 12,
plot_margin = margin(5, 10, 5, 10),
axis_title_size = 9,
axis_text_size = 8
) + theme(legend.position = "none")
) Error in h(simpleError(msg, call)): erreur d'�valuation de l'argument 'x' lors de la s�lection d'une m�thode pour la fonction '%in%' : objet 'Type' introuvable
MiscMetabar::accu_plot_balanced_modality(d_pq, factor_of_interest, nperm=20) + theme_idest()`set.seed(1)` was used to initialize repeatable random subsampling.
Please record this for your records so others can reproduce.
Try `set.seed(1); .Random.seed` for the full vector
...
Error in validObject(.Object): objet de classe "sample_data" incorrect: Sample Data must have non-zero dimensions.
ggbetween_pq(d_pq, factor_of_interest)Error in h(simpleError(msg, call)): erreur d'�valuation de l'argument 'object' lors de la s�lection d'une m�thode pour la fonction 'sample_data' : colonnes non définies sélectionnées
Session information are detailed below. More information about the machine, the system, as well as python and R packages, are available in the file data_final/information_run.txt .
sessionInfo()R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Debian GNU/Linux 12 (bookworm)
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0
locale:
[1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C
[3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8
[5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8
[7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Paris
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] MiscMetabar_0.10.1 purrr_1.0.2 dplyr_1.1.4 dada2_1.34.0
[5] Rcpp_1.0.13-1 ggplot2_3.5.1 phyloseq_1.50.0 targets_1.9.0
[9] knitr_1.49
loaded via a namespace (and not attached):
[1] bitops_1.0-9 deldir_2.0-4
[3] permute_0.9-7 rlang_1.1.4
[5] magrittr_2.0.3 ade4_1.7-22
[7] matrixStats_1.4.1 compiler_4.4.2
[9] mgcv_1.9-1 png_0.1-8
[11] callr_3.7.6 vctrs_0.6.5
[13] reshape2_1.4.4 stringr_1.5.1
[15] pwalign_1.2.0 pkgconfig_2.0.3
[17] crayon_1.5.3 fastmap_1.2.0
[19] backports_1.5.0 XVector_0.46.0
[21] utf8_1.2.4 Rsamtools_2.22.0
[23] rmarkdown_2.29 UCSC.utils_1.2.0
[25] ps_1.8.1 xfun_0.49
[27] zlibbioc_1.52.0 GenomeInfoDb_1.42.0
[29] jsonlite_1.8.9 biomformat_1.34.0
[31] rhdf5filters_1.18.0 DelayedArray_0.32.0
[33] Rhdf5lib_1.28.0 BiocParallel_1.40.0
[35] jpeg_0.1-10 parallel_4.4.2
[37] cluster_2.1.6 R6_2.5.1
[39] RColorBrewer_1.1-3 stringi_1.8.4
[41] GenomicRanges_1.58.0 SummarizedExperiment_1.36.0
[43] iterators_1.0.14 IRanges_2.40.0
[45] Matrix_1.7-1 splines_4.4.2
[47] igraph_2.1.1 tidyselect_1.2.1
[49] abind_1.4-8 yaml_2.3.10
[51] vegan_2.6-8 codetools_0.2-20
[53] hwriter_1.3.2.1 processx_3.8.4
[55] lattice_0.22-6 tibble_3.2.1
[57] plyr_1.8.9 Biobase_2.66.0
[59] withr_3.0.2 ShortRead_1.64.0
[61] evaluate_1.0.1 survival_3.7-0
[63] RcppParallel_5.1.9 Biostrings_2.74.0
[65] pillar_1.9.0 BiocManager_1.30.25
[67] MatrixGenerics_1.18.0 renv_1.0.11
[69] foreach_1.5.2 stats4_4.4.2
[71] generics_0.1.3 rprojroot_2.0.4
[73] S4Vectors_0.44.0 munsell_0.5.1
[75] scales_1.3.0 base64url_1.4
[77] glue_1.8.0 tools_4.4.2
[79] interp_1.1-6 data.table_1.16.2
[81] GenomicAlignments_1.42.0 rhdf5_2.50.0
[83] grid_4.4.2 ape_5.8
[85] latticeExtra_0.6-30 colorspace_2.1-1
[87] nlme_3.1-166 GenomeInfoDbData_1.2.13
[89] cli_3.6.3 fansi_1.0.6
[91] S4Arrays_1.6.0 gtable_0.3.6
[93] digest_0.6.37 BiocGenerics_0.52.0
[95] SparseArray_1.6.0 htmlwidgets_1.6.4
[97] htmltools_0.5.8.1 multtest_2.62.0
[99] lifecycle_1.0.4 here_1.0.1
[101] httr_1.4.7 secretbase_1.0.3
[103] MASS_7.3-61
@online{taudière2024,
author = {Taudière, Adrien},
title = {Alpha-Diversity},
date = {2024-11-25},
langid = {en}
}